Experimental evolution of recombining E. coli on novel nutrient

Here we evolved six replicate populations of either highly recombining Rec+or lowly recombining Rec- E. coli strains on the carbon source L-arabinose and the amino acid precursor indole. The experiments ancestral strains are not viable on these nutrients, but 130 generations of adaptive evolution were sufficient to render them viable. Recombination conferred a more pronounced advantage to populations adapting to indole. To study the genomic changes associated with this advantage, we sequenced the genomes of 384 clones isolated from selected replicates at the end of the experiment. These genomes harbor complex changes that range from point mutations to large- scale DNA amplifications. Among several candidate adaptive point mutations, those in the tryptophanase gene tnaC stand out, because the tna operon in which it resides has a known role in indole metabolism. One of the highly recombining populations also shows a significant excess of large-scale segmental DNA amplifications that include the tna operon. Moreover, this lineage shows a unique and adaptive combination of point mutations and DNA amplifications that originated independently from one another, and were likely joined by recombination.Our data illustrate that the advantages of recombination for adaptive evolution strongly depends on the environment, and that they can be associated with complex genomic changes.